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Human CD73 (ecto 5'-nucleotidase) in complex with PSB12676 (an AOPCP derivative, compound 9 in paper) in the closed state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H2I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 Drop: 3 mg/ml CD73, 100 microM ZnCl2 and 1 mM of compound. Reservoir: 5-8 percent (w/v) polyethylene glycol 6000, 0.1 M NaMES pH 5.5. Cryo buffer: 25 percent PEG200, 0.1 M NaMES pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.62 53.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.519 α = 90 b = 97.453 β = 90 c = 233.697 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2015-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.6 47.7 99.8 0.354 0.385 0.149 0.989 5.7 6.6 19655 69.67
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.72 99.9 3.881 4.223 1.653 0.234 6.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 4h2i 2.6 47.7 19612 528 99.8 0.217 0.216 0.2507 0.249 0.2857 RANDOM 95.59
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 19.5777 -44.0576 24.4799
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.36 t_omega_torsion 3.09 t_angle_deg 1.06 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.36 t_omega_torsion 3.09 t_angle_deg 1.06 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4022 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 47
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PDB_EXTRACT data extraction BUSTER phasing